1. Phylogenetic trees
- Author
-
Elizabeth Gross, Hector Baños, Robert Krone, Nathaniel Bushek, Colby Long, Ruth Davidson, Robert Walker, Pamela E. Harris, and Allen Stewart
- Subjects
Theoretical computer science ,Ideal (set theory) ,Phylogenetic tree ,Computer science ,Group (mathematics) ,010102 general mathematics ,0206 medical engineering ,Dimension (graph theory) ,Populations and Evolution (q-bio.PE) ,02 engineering and technology ,Algebraic geometry ,16. Peace & justice ,01 natural sciences ,Upper and lower bounds ,Tree (descriptive set theory) ,Mathematics - Algebraic Geometry ,FOS: Biological sciences ,Generating set of a group ,FOS: Mathematics ,Computer Science::Mathematical Software ,0101 mathematics ,Quantitative Biology - Populations and Evolution ,Algebraic Geometry (math.AG) ,020602 bioinformatics ,Computer Science::Databases - Abstract
We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.
- Published
- 2016